A field-based comparative experiment between rice monoculture （RM） and rice-crayfishfarming models（RC） was conducted to study the effects of introducing crayfish （Procambarus clarkii） into paddy fields on the microbial diversity and the carbon sequestration in soil.The impacts of different rice cultivation models on the diversity and stability of microbial community，and the fractions of organic carbon in the topsoil （0-20 cm） and subsoil （20-40 cm） were investigated.The results showed that the content of organic carbon in topsoil under the RC was 7.3% higher than that under RM，with a significant increase of 35.8% in the content of organic carbon in subsoil.The diversity of fungal community in the subsoil significantly decreased，with a decrease in the index of Chao1，Richness，and ACE indexes of 6.9%，7.2%，and 8.7%，respectively，while there was no significant effect on the diversity of microbial community in the topsoil.The RC significantly enhanced the network size，connectivity，and average degree of co-occurrence networks for bacteria and fungi in both topsoil and subsoil，thereby improving the stability of network.It is indicated that the RC significantly increases the accumulation of organic carbon and the stability of microbial community in subsoil，promoting the biological fertility in paddy soil.